A death row prisoner in Alabama has had a final plea against execution turned down by the federal appeals court on the grounds that his lawyers failed to meet a 42-day deadline to file legal paperwork.

Cory Maples, 35, may go to his death as a result of a procedural mistake by his lawyers of which he had no knowledge or he had no control.

The case has highlighted inconsistencies in the application of the death penalty across America: critics say the system is so skewed that issues of justice and fairness are frequently lost in a myopic focus on bureaucratic rule-keeping.

"We have created an incredibly complex procedural maze, with the result that we are risking executing people who should not have been given a death sentence in the first place," said Bryan Stevenson, director of the Alabama-based Equal Justice Initiative, EJI.

The case of Maples began on 7 July 1995 when two friends, Stacy Terry and Barry Robinson, went round to his house. Later, as the men were leaving in their car, Maples shot them both twice in the head with his father's gun. He confessed to the murders, telling police he had drunk about eight pints of beer.

At his trial, Maples was found guilty by 10 votes to two and the jury recommended death. Just one fewer vote against him would have spared him under Alabama law.

After Maples was sent to death row in 2000 he took on another team of lawyers for post-conviction appeals. They found that his original lawyer had made basic and serious mistakes.

He had failed to present the jury with evidence that Maples had been drunk, or that he had a history of mental illness, suicide attempts and drug addiction, to such an extent that he was mentally incapable of carrying out a premeditated murder and was thus unfit to face the death penalty.

His new lawyers, at a large international firm called Sullivan & Cromwell, went before the Alabama courts to argue that Maples's trial lawyer had mishandled his defence, but in 2003 a judge rejected the petition. They then had 42 days to file a further appeal.

Paperwork was mailed from Alabama to their New York offices, addressed to two lawyers who had left the company. The letter was returned unopened to the Alabama courts and the deadline missed.

Sullivan & Cromwell said it could not comment as the case, which it continues to work on, is still active. After prolonged legal wrangling, the federal appeals court has ruled that because the deadline was missed, Maples has lost the right to a final appeal against being put to death. "Any and all fault here lies with Maples for not filing a timely notice of appeal," the ruling says.

One judge, Rosemary Barkett, dissented from the ruling, saying "the interests of justice require that Maples be permitted review of his claims. This court is allowing him to be put to death because of the negligence" of his lawyers.

Death row campaigners say the Maples case highlights the brutal, legalistic approach to execution adopted in Alabama and a handful of other states. Alabama has 200 death row prisoners, and holds the record in the country for the number of people sentenced to death each year in recent times.

Yet it is the only state in America that has no public defender programme, which means that people charged with offences that could lead to the death penalty have no right to choose a lawyer for themselves. Instead, they are handed a lawyer by Alabama state, some of whom, according to EJI, have fallen asleep or been drunk during trials.

At the time Maples went on trial there was a limit on out-of-court preparation costs for the state-appointed lawyer, who was given just $1,000 (£625) to prepare for the case. "When you pay someone this kind of money you have every reason to think the lawyer is not going to do effective work," Stevenson said.

The result, he added, was that the burden of responsibility was placed on death row prisoners themselves – many of whom are poorly educated or mentally ill – to negotiate the legal maze.

"The crazy situation is that we execute someone according to whether documents were filed on a Thursday or Friday, or if the Ts were cross and the Is dotted," he said.